| gene transfer in magnetic bacteria: transposon mutagenesis and cloning of genomic dna fragments required for magnetosome synthesis. | broad-host-range incp and incq plasmids have been transferred to the aerobic magnetic bacterium aquaspirillum sp. strain amb-1. conjugal matings with escherichia coli s17-1 allowed high-frequency transfer of the rk2 derivative prk415 (4.5 x 10(-3) transconjugant per recipient cell) and the rsf1010 derivative pkt230 (3.0 x 10(-3) transconjugant per recipient). these plasmids successfully formed autonomous replicons in transconjugants and could be isolated and transformed back into e. coli, illust ... | 1992 | 1314800 |
| nucleotide sequence of reca gene of aquaspirillum magnetotacticum. | | 1990 | 2106674 |
| hydroxamate production by aquaspirillum magnetotacticum. | spent culture fluids from aquaspirillum magnetotacticum ms-1 grown at high (20 microm) but not low (5 microm) iron concentration contained material yielding a positive hydroxamate test. cells possessed six major outer membrane proteins. three outer membrane proteins ranging from 72,000 to 85,000 daltons were coordinately produced at iron concentrations conducive to hydroxamate production. a 55,000-dalton iron-repressible outer membrane protein was also present in strain ms-1 cultured at low but ... | 1986 | 2941414 |
| iron respiration-driven proton translocation in aerobic bacteria. | washed cell suspensions of aquaspirillum magnetotacticum ms-1, a. itersonii e12639, bacillus subtilis 6633, and escherichia coli csh27 translocated protons in response to the added oxidant o2 or no3-, with triphenylmethylphosphonium bromide as the permeant ion. iron respiration-driven proton translocation was observed in a. magnetotacticum ms-1, b. subtilis, and e. coli but not in a nonmagnetic strain of a. magnetotacticum (strain nm-1a) or with a. itersonii. proton translocation to fe3+ was tot ... | 1986 | 3015890 |
| characterization of the bacterial magnetosome membrane. | intact magnetosomes of aquaspirillum magnetotacticum were purified from broken cells by a magnetic separation technique. electron microscopic and chemical analyses revealed the magnetite to be enclosed by a lipid bilayer admixed with proteins. lipids were recovered in fractions expected to contain (i) neutral lipids and free fatty acids, (ii) glycolipids and sulfolipids, and (iii) phospholipids (in a weight ratio of 1:4:6). phospholipids included phosphatidylserine and phosphatidylethanolamine. ... | 1988 | 3123464 |
| magnetosome dynamics in magnetotactic bacteria. | diffusive motions of the magnetosomes (enveloped fe3o4 particles) in the magnetotactic bacterium aquaspirillum magnetotacticum result in a very broad-line mössbauer spectrum (t approximately 100 mm/s) above freezing temperatures. the line width increases with increasing temperature. the data are analyzed using a bounded diffusion model to yield the rotational and translational motions of the magnetosomes as well as the effective viscosity of the material surrounding the magnetosomes. the results ... | 1984 | 6743757 |
| evolutionary relationships among magnetospirillum strains inferred from phylogenetic analysis of 16s rdna sequences. | we have investigated the evolutionary relationships between two facultatively anaerobic magnetospirillum strains (amb-1 and mgt-1) and fastidious, obligately microaerophilic species, such as magnetospirillum magnetotacticum, using a molecular phylogenetic approach. genomic dna from strains mgt-1 and amb-1 was used as a template for amplification of the genes coding for 16s rrna (16s rdna) by the polymerase chain reaction. amplified dna fragments were sequenced (1,424 bp) and compared with sequen ... | 1993 | 7691800 |
| the reca protein as a model molecule for molecular systematic studies of bacteria: comparison of trees of recas and 16s rrnas from the same species. | the evolution of the reca protein was analyzed using molecular phylogenetic techniques. phylogenetic trees of all currently available complete reca proteins were inferred using multiple maximum parsimony and distance matrix methods. comparison and analysis of the trees reveal that the inferred relationships among these proteins are highly robust. the reca trees show consistent subdivisions corresponding to many of the major bacterial groups found in trees of other molecules including the alpha, ... | 1995 | 8587109 |
| dynamics of iron uptake and fe3o4 biomineralization during aerobic and microaerobic growth of magnetospirillum gryphiswaldense. | iron uptake and magnetite (fe3o4) crystal formation could be studied in the microaerophilic magnetic bacterium magnetospirillum gryphiswaldense by using a radioactive tracer method for iron transport and a differential light-scattering technique for magnetism. magnetite formation occurred only in a narrow range of low oxygen concentration, i.e., 2 to 7 microm o2 at 30 degrees c. magnetic cells stored up to 2% iron as magnetite crystals in intracytoplasmic vesicles. this extraordinary uptake of i ... | 1998 | 9422606 |
| comparison of phenotypic and genotypic techniques for identification of unusual aerobic pathogenic gram-negative bacilli. | rapid and accurate identification of bacterial pathogens is a fundamental goal of clinical microbiology, but one that is difficult or impossible for many slow-growing and fastidious organisms. we used identification systems based on cellular fatty acid profiles (sherlock; midi, inc., newark, del.), carbon source utilization (microlog; biolog, inc., hayward, calif.), and 16s rrna gene sequence (microseq; perkin-elmer applied biosystems division, foster city, calif.) to evaluate 72 unusual aerobic ... | 1998 | 9817894 |
| identification of seven treponema species in health- and disease-associated dental plaque by nested pcr. | species-specific nested pcr was used to detect treponema amylovorum, treponema denticola, treponema maltophilum, treponema medium, treponema pectinovorum, treponema socranskii, and treponema vincentii in dental plaque. subjects with periodontitis harbored all species, but t. pectinovorum and t. vincentii were not found in plaque from disease-free subjects. | 1999 | 9986879 |
| iron reductase for magnetite synthesis in the magnetotactic bacterium magnetospirillum magnetotacticum. | ferric iron reductase was purified from magnetotactic bacterium magnetospirillum (formerly aquaspirillum) magnetotacticum (atcc 31632) to an electrophoretically homogeneous state. the enzyme was loosely bound on the cytoplasmic face of the cytoplasmic membrane and was found more frequently in magnetic cells than in nonmagnetic cells. the molecular mass of the purified enzyme was calculated upon sodium dodecyl sulfate-polyacrylamide gel electrophoresis to be about 36 kda, almost the same as that ... | 1999 | 10094692 |
| bacterioferritin a modulates catalase a (kata) activity and resistance to hydrogen peroxide in pseudomonas aeruginosa. | we have cloned a 3.6-kb genomic dna fragment from pseudomonas aeruginosa harboring the rpoa, rplq, kata, and bfra genes. these loci are predicted to encode, respectively, (i) the alpha subunit of rna polymerase; (ii) the l17 ribosomal protein; (iii) the major catalase, kata; and (iv) one of two iron storage proteins called bacterioferritin a (bfra; cytochrome b1 or b557). our goal was to determine the contributions of kata and bfra to the resistance of p. aeruginosa to hydrogen peroxide (h2o2). ... | 1999 | 10368148 |
| phenotypic and genotypic heterogeneity among cultivable pathogen-related oral spirochetes and treponema vincentii. | recent findings challenge the assumption that pathogen-related oral spirochetes (pros) are related to treponema pallidum. treponema vincentii, grown in omiz-pat media, cross-reacted with monoclonal antibody h9-2 against t. pallidum, and cultivable pros had 16s rrna gene sequences similar to those of t. vincentii (c.-b. choi, c. wyss, and u. b. göbel. j. clin. microbiol. 34:1922-1925, 1996). aims of the present study were to determine whether antigen phenotypes of oral treponemas were influenced ... | 1999 | 10523573 |
| ubiquity and diversity of dissimilatory (per)chlorate-reducing bacteria. | environmental contamination with compounds containing oxyanions of chlorine, such as perchlorate or chlorate [(per)chlorate] or chlorine dioxide, has been a constantly growing problem over the last 100 years. although the fact that microbes reduce these compounds has been recognized for more than 50 years, only six organisms which can obtain energy for growth by this metabolic process have been described. as part of a study to investigate the diversity and ubiquity of microorganisms involved in ... | 1999 | 10583970 |
| bacterial primary colonization and early succession on surfaces in marine waters as determined by amplified rrna gene restriction analysis and sequence analysis of 16s rrna genes. | the nearly universal colonization of surfaces in marine waters by bacteria and the formation of biofilms and biofouling communities have important implications for ecological function and industrial processes. however, the dynamics of surface attachment and colonization in situ, particularly during the early stages of biofilm establishment, are not well understood. experimental surfaces that differed in their degrees of hydrophilicity or hydrophobicity were incubated in a salt marsh estuary tida ... | 2000 | 10653705 |
| isolation and characterization of a new denitrifying spirillum capable of anaerobic degradation of phenol. | two kinds of phenol-degrading denitrifying bacteria, azoarcus sp. strain cc-11 and spiral bacterial strain cc-26, were isolated from the same enrichment culture after 1 and 3 years of incubation, respectively. both strains required ferrous ions for growth, but strain cc-26 grew better than strain cc-11 grew under iron-limited conditions, which may have resulted in the observed change in the phenol-degrading bacteria during the enrichment process. strain cc-26 grew on phenol, benzoate, and other ... | 2000 | 10742201 |
| rubrerythrin and rubredoxin oxidoreductase in desulfovibrio vulgaris: a novel oxidative stress protection system. | evidence is presented for an alternative to the superoxide dismutase (sod)-catalase oxidative stress defense system in desulfovibrio vulgaris (strain hildenborough). this alternative system consists of the nonheme iron proteins, rubrerythrin (rbr) and rubredoxin oxidoreductase (rbo), the product of the rbo gene (also called desulfoferrodoxin). a deltarbo strain of d. vulgaris was found to be more sensitive to internal superoxide exposure than was the wild type. unlike rbo, expression of plasmid- ... | 2001 | 11114906 |
| a large gene cluster encoding several magnetosome proteins is conserved in different species of magnetotactic bacteria. | in magnetotactic bacteria, a number of specific proteins are associated with the magnetosome membrane (mm) and may have a crucial role in magnetite biomineralization. we have cloned and sequenced the genes of several of these polypeptides in the magnetotactic bacterium magnetospirillum gryphiswaldense that could be assigned to two different genomic regions. except for mama, none of these genes have been previously reported to be related to magnetosome formation. homologous genes were found in th ... | 2001 | 11571158 |
| a repressor protein, phar, regulates polyhydroxyalkanoate (pha) synthesis via its direct interaction with pha. | phasins (phap) are predominantly polyhydroxyalkanoate (pha) granule-associated proteins that positively affect pha synthesis. recently, we reported that the phar gene, which is located downstream of phap in paracoccus denitrificans, codes for a negative regulator involved in phap expression. in this study, dnase i footprinting revealed that phar specifically binds to two regions located upstream of phap and phar, suggesting that phar plays a role in the regulation of phap expression as well as a ... | 2002 | 12081972 |
| regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation. | the riboflavin biosynthesis in bacteria was analyzed using comparative analysis of genes, operons and regulatory elements. a model for regulation based on formation of alternative rna structures involving the rfn elements is suggested. in gram-positive bacteria including actinomycetes, thermotoga, thermus and deinococcus, the riboflavin metabolism and transport genes are predicted to be regulated by transcriptional attenuation, whereas in most gram-negative bacteria, the riboflavin biosynthesis ... | 2002 | 12136096 |
| functional annotation of class i lysyl-trna synthetase phylogeny indicates a limited role for gene transfer. | functional and comparative genomic studies have previously shown that the essential protein lysyl-trna synthetase (lysrs) exists in two unrelated forms. most prokaryotes and all eukaryotes contain a class ii lysrs, whereas most archaea and a few bacteria contain a less common class i lysrs. in bacteria the class i lysrs is only found in the alpha-proteobacteria and a scattering of other groups, including the spirochetes, while the class i protein is by far the most common form of lysrs in archae ... | 2002 | 12142429 |
| predicted structure and phyletic distribution of the rna-binding protein hfq. | hfq, a bacterial rna-binding protein, was recently shown to contain the sm1 motif, a characteristic of sm and lsm proteins that function in rna processing events in archaea and eukaryotes. in this report, comparative structural modeling was used to predict a three-dimensional structure of the hfq core sequence. the predicted structure aligns with most major features of the methanobacterium thermoautotrophicum lsm protein structure. conserved residues in hfq are positioned at the same structural ... | 2002 | 12202750 |
| sequencing and transcriptional analysis of the chlorite dismutase gene of dechloromonas agitata and its use as a metabolic probe. | the dismutation of chlorite into chloride and o(2) represents a central step in the reductive pathway of perchlorate that is common to all dissimilatory perchlorate-reducing bacteria and is mediated by a single enzyme, chlorite dismutase. the chlorite dismutase gene cld was isolated and sequenced from the perchlorate-reducing bacterium dechloromonas agitata strain ckb. sequence analysis identified an open reading frame of 834 bp that would encode a mature protein with an n-terminal sequence iden ... | 2002 | 12324326 |
| genes coding for a new pathway of aerobic benzoate metabolism in azoarcus evansii. | a new pathway for aerobic benzoate oxidation has been postulated for azoarcus evansii and for a bacillus stearothermophilus-like strain. benzoate is first transformed into benzoyl coenzyme a (benzoyl-coa), which subsequently is oxidized to 3-hydroxyadipyl-coa and then to 3-ketoadipyl-coa; all intermediates are coa thioesters. the genes coding for this benzoate-induced pathway were investigated in the beta-proteobacterium a. evansii. they were identified on the basis of n-terminal amino acid sequ ... | 2002 | 12399500 |
| a polyphosphate kinase (ppk2) widely conserved in bacteria. | synthesis of inorganic polyphosphate (poly p) from the terminal phosphate of atp is catalyzed reversibly by poly p kinase (ppk, now designated ppk1) initially isolated from escherichia coli. ppk1 is highly conserved in many bacteria, including some of the major pathogens such as pseudomonas aeruginosa. in a null mutant of p. aeruginosa lacking ppk1, we have discovered a previously uncharacterized ppk activity (designated ppk2) distinguished from ppk1 by the following: synthesis of poly p from gt ... | 2002 | 12486232 |
| lateral gene transfer and ancient paralogy of operons containing redundant copies of tryptophan-pathway genes in xylella species and in heterocystous cyanobacteria. | tryptophan-pathway genes that exist within an apparent operon-like organization were evaluated as examples of multi-genic genomic regions that contain phylogenetically incongruous genes and coexist with genes outside the operon that are congruous. a seven-gene cluster in xylella fastidiosa includes genes encoding the two subunits of anthranilate synthase, an aryl-coa synthetase, and trpr. a second gene block, present in the anabaena/nostoc lineage, but not in other cyanobacteria, contains a near ... | 2003 | 12620124 |
| identification and characterization of transposable elements of paracoccus pantotrophus. | we studied diversity and distribution of transposable elements residing in different strains (dsm 11072, dsm 11073, dsm 65, and lmd 82.5) of a soil bacterium paracoccus pantotrophus (alpha-proteobacteria). with application of a shuttle entrapment vector pmec1, several novel insertion sequences (iss) and transposons (tns) have been identified. they were sequenced and subjected to detailed comparative analysis, which allowed their characterization (i.e., identification of transposase genes, termin ... | 2003 | 12813068 |
| characterization of a new lexa binding motif in the marine magnetotactic bacterium strain mc-1. | mc-1 is a marine, magnetotactic bacterium that is phylogenetically associated with the alpha subclass of the proteobacteria and is the first and only magnetotactic coccus isolated in pure culture to date. by using a tblastn search, a lexa gene was identified in the published genome of mc-1; it was subsequently cloned, and the protein was purified to >90% purity. results from reverse transcription-pcr analysis revealed that the mc-1 lexa gene comprises a single transcriptional unit with two open ... | 2003 | 12867456 |
| expression cloning and biochemical characterization of a rhizobium leguminosarum lipid a 1-phosphatase. | lipid a of rhizobium leguminosarum, a nitrogen-fixing plant endosymbiont, displays several significant structural differences when compared with escherichia coli. an especially striking feature of r. leguminosarum lipid a is that it lacks both the 1- and 4'-phosphate groups. distinct lipid a phosphatases that attack either the 1 or the 4' positions have previously been identified in extracts of r. leguminosarum and rhizobium etli but not sinorhizobium meliloti or e. coli. here we describe the id ... | 2003 | 12869541 |
| stability of a 24-meric homopolymer: comparative studies of assembly-defective mutants of rhodobacter capsulatus bacterioferritin and the native protein. | the stability of rhodobacter capsulatus bacterioferritin, a 24-meric homopolymer, toward denaturation on variation in ph and temperature, and increasing concentrations of urea and guanidine.hcl was investigated with native page, and cd and fluorescence spectroscopies. with temperature and urea, the wild-type protein denatured without discernible intermediates in the equilibrium experiments, but with guanidine.hcl (gnd.hcl) one or more intermediate species were apparent at relatively low gnd.hcl ... | 2003 | 12876316 |
| application of comparative genomics in the identification and analysis of novel families of membrane-associated receptors in bacteria. | a great diversity of multi-pass membrane receptors, typically with 7 transmembrane (tm) helices, is observed in the eukaryote crown group. so far, they are relatively rare in the prokaryotes, and are restricted to the well-characterized sensory rhodopsins of various phototropic prokaryotes. | 2003 | 12914674 |
| the is1111 family members is4321 and is5075 have subterminal inverted repeats and target the terminal inverted repeats of tn21 family transposons. | is5075 and is4321 are closely related (93.1% identical) members of the is1111 family that target a specific position in the 38-bp terminal inverted repeats of tn21 family transposons and that are inserted in only one orientation. they are 1,327 bp long and have identical ends consisting of short inverted repeats of 12 bp with an additional 7 bp (taatgag) or 6 bp (aatgag) to the left of the left inverted repeats and 3 bp (aga) or 4 bp (agat) to the right of the right inverted repeat. circular for ... | 2003 | 14563872 |
| sequencing and characterization of pbm400 from bacillus megaterium qm b1551. | bacillus megaterium qm b1551 plasmid pbm400, one of seven indigenous plasmids, has been labeled with a selectable marker, isolated, completely sequenced, and partially characterized. a sequence of 53,903 bp was generated, revealing a total of 50 predicted open reading frames (orfs); 33 were carried on one strand and 17 were carried on the other. these orfs comprised 57% of the pbm400 sequence. besides the replicon region and a complete rrna operon that have previously been described, several int ... | 2003 | 14602653 |
| coevolution of an aminoacyl-trna synthetase with its trna substrates. | glutamyl-trna synthetases (glurss) occur in two types, the discriminating and the nondiscriminating enzymes. they differ in their choice of substrates and use either trnaglu or both trnaglu and trnagln. although most organisms encode only one glurs, a number of bacteria encode two different glurs proteins; yet, the trna specificity of these enzymes and the reason for such gene duplications are unknown. a database search revealed duplicated glurs genes in >20 bacterial species, suggesting that th ... | 2003 | 14615592 |
| new connections in the prokaryotic toxin-antitoxin network: relationship with the eukaryotic nonsense-mediated rna decay system. | several prokaryotic plasmids maintain themselves in their hosts by means of diverse post-segregational cell killing systems. recent findings suggest that chromosomally encoded copies of toxins and antitoxins of post-segregational cell killing systems - such as the rele system - might function as regulatory switches under stress conditions. the rele toxin cleaves ribosome-associated transcripts, whereas another post-segregational cell killing toxin, pare, functions as a gyrase inhibitor. | 2003 | 14659018 |
| metagenome survey of biofilms in drinking-water networks. | most naturally occurring biofilms contain a vast majority of microorganisms which have not yet been cultured, and therefore we have little information on the genetic information content of these communities. therefore, we initiated work to characterize the complex metagenome of model drinking water biofilms grown on rubber-coated valves by employing three different strategies. first, a sequence analysis of 650 16s rrna clones indicated a high diversity within the biofilm communities, with the ma ... | 2003 | 14660379 |
| characterization of the 101-kilobase-pair megaplasmid pkb1, isolated from the rubber-degrading bacterium gordonia westfalica kb1. | the complete sequence of the circular 101,016-bp megaplasmid pkb1 from the cis-1,4-polyisoprene-degrading bacterium gordonia westfalica kb1, which represents the first described extrachromosomal dna of a member of this genus, was determined. plasmid pkb1 harbors 105 open reading frames. the predicted products of 46 of these are significantly related to proteins of known function. plasmid pkb1 is organized into three functional regions that are flanked by insertion sequence (is) elements: (i) a r ... | 2004 | 14679241 |
| complete sequence and evolutionary genomic analysis of the pseudomonas aeruginosa transposable bacteriophage d3112. | bacteriophage d3112 represents one of two distinct groups of transposable phage found in the clinically relevant, opportunistic pathogen pseudomonas aeruginosa. to further our understanding of transposable phage in p. aeruginosa, we have sequenced the complete genome of d3112. the genome is 37,611 bp, with an overall g+c content of 65%. we have identified 53 potential open reading frames, including three genes (the c repressor gene and early genes a and b) that have been previously characterized ... | 2004 | 14702309 |
| the hwe histidine kinases, a new family of bacterial two-component sensor kinases with potentially diverse roles in environmental signaling. | two-component signal transduction pathways play a major role in the response of bacteria to external cues. these pathways are initiated by large collection of histidine kinases (hks) containing a sensor domain that perceives the environmental signal followed by an hk domain that triggers a histidine-aspartate phosphorelay. previous phylogenetic analyses identified 11 major families of two-component hks by comparing signature motifs within the hk domain. here we describe a new family with homolog ... | 2004 | 14702314 |
| sequence analysis of the mobile genome island pklc102 of pseudomonas aeruginosa c. | the pseudomonas aeruginosa plasmid pklc102 coexists as a plasmid and a genome island in clone c strains. whereas the related plasmid pklk106 reversibly recombines with p. aeruginosa clone k chromosomes at one of the two trna(lys) genes, pklc102 is incorporated into the trna(lys) gene only close to the pila locus. targeting of the other trna(lys) copy in the chromosome is blocked by a 23,395-bp mosaic of truncated pao open reading frames, transposons, and pklc102 homologs. annotation and phylogen ... | 2004 | 14702321 |
| biochemical and proteomic analysis of the magnetosome membrane in magnetospirillum gryphiswaldense. | we analyzed the biochemical composition of the magnetosome membrane (mm) in magnetospirillum gryphiswaldense. isolated magnetosomes were associated with phospholipids and fatty acids which were similar to phospholipids and fatty acids from other subcellular compartments (i.e., outer and cytoplasmic membranes) but were present in different proportions. the binding characteristics of mm-associated proteins were studied by selective solubilization and limited proteolysis. the mm-associated proteins ... | 2004 | 14766587 |
| phosphatidylethanolamine is not essential for growth of sinorhizobium meliloti on complex culture media. | in addition to phosphatidylglycerol (pg), cardiolipin (cl), and phosphatidylethanolamine (pe), sinorhizobium meliloti also possesses phosphatidylcholine (pc) as a major membrane lipid. the biosynthesis of pc in s. meliloti can occur via two different routes, either via the phospholipid n-methylation pathway, in which pe is methylated three times in order to obtain pc, or via the phosphatidylcholine synthase (pcs) pathway, in which choline is condensed with cdp-diacylglycerol to obtain pc directl ... | 2004 | 14996797 |
| organization of lin genes and is6100 among different strains of hexachlorocyclohexane-degrading sphingomonas paucimobilis: evidence for horizontal gene transfer. | the organization of lin genes and is6100 was studied in three strains of sphingomonas paucimobilis (b90a, sp+, and ut26) which degraded hexachlorocyclohexane (hch) isomers but which had been isolated at different geographical locations. dna-dna hybridization data revealed that most of the lin genes in these strains were associated with is6100, an insertion sequence classified in the is6 family and initially found in mycobacterium fortuitum. eleven, six, and five copies of is6100 were detected in ... | 2004 | 15060023 |
| unraveling the function of the rhodospirillum rubrum activator of polyhydroxybutyrate (phb) degradation: the activator is a phb-granule-bound protein (phasin). | efficient hydrolysis of native poly(3-hydroxybutyrate) (nphb) granules in vitro by soluble phb depolymerase of rhodospirillum rubrum requires pretreatment of nphb with an activator compound present in r. rubrum cells (j. m. merrick and m. doudoroff, j. bacteriol. 88:60-71, 1964). edman sequencing of the purified activator (17.4 kda; matrix-assisted laser desorption ionization-time of flight mass spectrometry) revealed identity to a hypothetical protein deduced from a partially sequenced r. rubru ... | 2004 | 15060050 |
| inactivation of the flagellin gene flaa in magnetospirillum gryphiswaldense results in nonmagnetotactic mutants lacking flagellar filaments. | magnetotactic bacteria synthesize magnetosomes, which cause them to orient and migrate along magnetic field lines. the analysis of magnetotaxis and magnetosome biomineralization at the molecular level has been hindered by the unavailability of genetic methods, namely the lack of a means to introduce directed gene-specific mutations. here we report a method for knockout mutagenesis by homologous recombination in magnetospirillum gryphiswaldense. multiple flagellin genes, which are unlinked in the ... | 2004 | 15184166 |
| bacterial alpha2-macroglobulins: colonization factors acquired by horizontal gene transfer from the metazoan genome? | invasive bacteria are known to have captured and adapted eukaryotic host genes. they also readily acquire colonizing genes from other bacteria by horizontal gene transfer. closely related species such as helicobacter pylori and helicobacter hepaticus, which exploit different host tissues, share almost none of their colonization genes. the protease inhibitor alpha2-macroglobulin provides a major metazoan defense against invasive bacteria, trapping attacking proteases required by parasites for suc ... | 2004 | 15186489 |
| evidence that the algi/algj gene cassette, required for o acetylation of pseudomonas aeruginosa alginate, evolved by lateral gene transfer. | pseudomonas aeruginosa strains, isolated from chronically infected patients with cystic fibrosis, produce the o-acetylated extracellular polysaccharide, alginate, giving these strains a mucoid phenotype. o acetylation of alginate plays an important role in the ability of mucoid p. aeruginosa to form biofilms and to resist complement-mediated phagocytosis. the o-acetylation process is complex, requiring a protein with seven transmembrane domains (algi), a type ii membrane protein (algj), and a pe ... | 2004 | 15231808 |
| fur is involved in manganese-dependent regulation of mnta (sita) expression in sinorhizobium meliloti. | fur is a transcriptional regulator involved in iron-dependent control of gene expression in many bacteria. in this work we analyzed the phenotype of a fur mutant in sinorhizobium meliloti, an alpha-proteobacterium that fixes n(2) in association with host plants. we demonstrated that some functions involved in high-affinity iron transport, siderophore production, and iron-regulated outer membrane protein expression respond to iron in a fur-independent manner. however, manganese-dependent expressi ... | 2004 | 15240318 |
| polyhydroxyalkanoate (pha) accumulation in sulfate-reducing bacteria and identification of a class iii pha synthase (phaec) in desulfococcus multivorans. | seven strains of sulfate-reducing bacteria (srb) were tested for the accumulation of polyhydroxyalkanoates (phas). during growth with benzoate desulfonema magnum accumulated large amounts of poly(3-hydroxybutyrate) [poly(3hb)]. desulfosarcina variabilis (during growth with benzoate), desulfobotulus sapovorans (during growth with caproate), and desulfobacterium autotrophicum (during growth with caproate) accumulated poly(3hb) that accounted for 20 to 43% of cell dry matter. desulfobotulus sapovor ... | 2004 | 15294771 |
| identification of an na(+)-dependent transporter associated with saxitoxin-producing strains of the cyanobacterium anabaena circinalis. | blooms of the freshwater cyanobacterium anabaena circinalis are recognized as an important health risk worldwide due to the production of a range of toxins such as saxitoxin (stx) and its derivatives. in this study we used hip1 octameric-palindrome repeated-sequence pcr to compare the genomic structure of phylogenetically similar australian isolates of a. circinalis. stx-producing and nontoxic cyanobacterial strains showed different hip1 (highly iterated octameric palindrome 1) dna patterns, and ... | 2004 | 15294806 |
| identification and transcriptional control of caulobacter crescentus genes encoding proteins containing a cold shock domain. | the cold shock proteins are small peptides that share a conserved domain, called the cold shock domain (csd), that is important for nucleic acid binding. the caulobacter crescentus genome has four csp genes that encode proteins containing csds. three of these (cspa, cspb, and cspc) encode peptides of about 7 kda and are very similar to the cold shock proteins of other bacteria. analysis by reverse transcription-pcr of the fourth gene (cspd), which was previously annotated as encoding a 7-kda pro ... | 2004 | 15317764 |
| the bzd gene cluster, coding for anaerobic benzoate catabolism, in azoarcus sp. strain cib. | we report here that the bzd genes for anaerobic benzoate degradation in azoarcus sp. strain cib are organized as two transcriptional units, i.e., a benzoate-inducible catabolic operon, bzdnopqmstuvwxyza, and a gene, bzdr, encoding a putative transcriptional regulator. the last gene of the catabolic operon, bzda, has been expressed in escherichia coli and encodes the benzoate-coenzyme a (coa) ligase that catalyzes the first step in the benzoate degradation pathway. the bzda enzyme is able to acti ... | 2004 | 15317781 |
| an energy taxis transducer promotes root colonization by azospirillum brasilense. | motility responses triggered by changes in the electron transport system are collectively known as energy taxis. in azospirillum brasilense, energy taxis was shown to be the principal form of locomotor control. in the present study, we have identified a novel chemoreceptor-like protein, named tlp1, which serves as an energy taxis transducer. the tlp1 protein is predicted to have an n-terminal periplasmic region and a cytoplasmic c-terminal signaling module homologous to those of other chemorecep ... | 2004 | 15375141 |
| maturation of the unusual single-cysteine (xxxch) mitochondrial c-type cytochromes found in trypanosomatids must occur through a novel biogenesis pathway. | the c-type cytochromes are characterized by the covalent attachment of haem to the polypeptide via thioether bonds formed from haem vinyl groups and, normally, the thiols of two cysteines in a cxxch motif. intriguingly, the mitochondrial cytochromes c and c1 from two euglenids and the trypanosomatidae contain only a single cysteine within the haem-binding motif (xxxch). there are three known distinct pathways by which c-type cytochromes are matured post-translationally in different organisms. th ... | 2004 | 15500440 |
| widespread presence of "bacterial-like" ppp phosphatases in eukaryotes. | in eukaryotes, ppp (protein phosphatase p) family is one of the two known protein phosphatase families specific for ser and thr. the role of ppp phosphatases in multiple signaling pathways in eukaryotic cell has been extensively studied. unlike eukaryotic ppp phosphatases, bacterial members of the family have broad substrate specificity or may even be tyr-specific. moreover, one group of bacterial ppps are diadenosine tetraphosphatases, indicating that bacterial ppp phosphatases may not necessar ... | 2004 | 15555063 |
| novel genes of the dsr gene cluster and evidence for close interaction of dsr proteins during sulfur oxidation in the phototrophic sulfur bacterium allochromatium vinosum. | seven new genes designated dsrljopnsr were identified immediately downstream of dsrabefhcmk, completing the dsr gene cluster of the phototrophic sulfur bacterium allochromatium vinosum d (dsm 180(t)). interposon mutagenesis proved an essential role of the encoded proteins for the oxidation of intracellular sulfur, an obligate intermediate during the oxidation of sulfide and thiosulfate. while dsrr and dsrs encode cytoplasmic proteins of unknown function, the other genes encode a predicted nadph: ... | 2005 | 15687204 |
| crystal structure and dna-binding analysis of reco from deinococcus radiodurans. | the recfor pathway has been shown to be essential for dna repair through the process of homologous recombination in bacteria and, recently, to be important in the recovery of stalled replication forks following uv irradiation. reco, along with recr, recf, recq and recj, is a principal actor in this fundamental dna repair pathway. here we present the three-dimensional structure of a member of the reco family. the crystal structure of deinococcus radiodurans reco (drreco) reveals possible binding ... | 2005 | 15719017 |
| identification of a new family of putative pd-(d/e)xk nucleases with unusual phylogenomic distribution and a new type of the active site. | prediction of structure and function for uncharacterized protein families by identification of evolutionary links to characterized families and known structures is one of the cornerstones of genomics. theoretical assignment of three-dimensional folds and prediction of protein function even at a very general level can facilitate the experimental determination of the molecular mechanism of action and the role that members of a given protein family fulfill in the cell. here, we predict the three-di ... | 2005 | 15720711 |
| functional domains of nosr, a novel transmembrane iron-sulfur flavoprotein necessary for nitrous oxide respiration. | bacterial nitrous oxide (n2o) respiration depends on the polytopic membrane protein nosr for the expression of n2o reductase from the nosz gene. we constructed his-tagged nosr and purified it from detergent-solubilized membranes of pseudomonas stutzeri atcc 14405. nosr is an iron-sulfur flavoprotein with redox centers positioned at opposite sides of the cytoplasmic membrane. the flavin cofactor is presumably bound covalently to an invariant threonine residue of the periplasmic domain. nosr also ... | 2005 | 15743947 |
| the presumptive magnetosome protein mms16 is a poly(3-hydroxybutyrate) granule-bound protein (phasin) in magnetospirillum gryphiswaldense. | the mms16 protein has been previously found to be associated with isolated magnetosomes from two magnetospirillum strains. a function of this protein as a magnetosome-specific gtpase involved in the formation of intracellular magnetosome membrane vesicles was suggested. here we present a study of the mms16 protein from magnetospirillum gryphiswaldense to clarify its function. insertion-duplication mutagenesis of the mms16 gene did not affect the formation of magnetosome particles but resulted in ... | 2005 | 15774885 |
| functional insights from the distribution and role of homopeptide repeat-containing proteins. | expansion of "low complex" repeats of amino acids such as glutamine (poly-q) is associated with protein misfolding and the development of degenerative diseases such as huntington's disease. the mechanism by which such regions promote misfolding remains controversial, the function of many repeat-containing proteins (rcps) remains obscure, and the role (if any) of repeat regions remains to be determined. here, a web-accessible database of rcps is presented. the distribution and evolution of rcps t ... | 2005 | 15805494 |
| 6s rna is a widespread regulator of eubacterial rna polymerase that resembles an open promoter. | 6s rna is an abundant noncoding rna in escherichia coli that binds to sigma70 rna polymerase holoenzyme to globally regulate gene expression in response to the shift from exponential growth to stationary phase. we have computationally identified >100 new 6s rna homologs in diverse eubacterial lineages. two abundant bacillus subtilis rnas of unknown function (bsra and bsrb) and cyanobacterial 6sa rnas are now recognized as 6s homologs. structural probing of e. coli 6s rna and a b. subtilis homolo ... | 2005 | 15811922 |
| genetic diversity of benzoyl coenzyme a reductase genes detected in denitrifying isolates and estuarine sediment communities. | benzoyl coenzyme a (benzoyl-coa) reductase is a central enzyme in the anaerobic degradation of organic carbon, which utilizes a common intermediate (benzoyl-coa) in the metabolism of many aromatic compounds. the diversity of benzoyl-coa reductase genes in denitrifying bacterial isolates capable of degrading aromatic compounds and in river and estuarine sediment samples from the arthur kill in new jersey and the chesapeake bay in maryland was investigated. degenerate primers were developed from t ... | 2005 | 15812036 |
| complete genome sequence of phihsic, a pseudotemperate marine phage of listonella pelagia. | the genome for the marine pseudotemperate member of the siphoviridae phihsic has been sequenced using a combination of linker amplification library construction, restriction digest library construction, and primer walking. phihsic enters into a pseudolysogenic relationship with its host, listonella pelagia, characterized by sigmoidal growth curves producing >10(9) cells/ml and >10(11) phage/ml. the genome (37,966 bp; g+c content, 44%) contained 47 putative open reading frames (orfs), 17 of which ... | 2005 | 15933034 |
| contribution of horizontal gene transfer to the evolution of saccharomyces cerevisiae. | the genomes of the hemiascomycetes saccharomyces cerevisiae and ashbya gossypii have been completely sequenced, allowing a comparative analysis of these two genomes, which reveals that a small number of genes appear to have entered these genomes as a result of horizontal gene transfer from bacterial sources. one potential case of horizontal gene transfer in a. gossypii and 10 potential cases in s. cerevisiae were identified, of which two were investigated further. one gene, encoding the enzyme d ... | 2005 | 15947202 |
| signature proteins that are distinctive of alpha proteobacteria. | the alpha (alpha) proteobacteria, a very large and diverse group, are presently characterized solely on the basis of 16s rrna trees, with no known molecular characteristic that is unique to this group. the genomes of three alpha-proteobacteria, rickettsia prowazekii (rp), caulobacter crescentus (cc) and bartonella quintana (bq), were analyzed in order to search for proteins that are unique to this group. | 2005 | 15960851 |
| identification, cloning, and expression of the camp-like factor autotransporter gene (cfa) of bartonella henselae. | the camp reaction was first described by christie et al. (r. christie, n. e. atkins, and e. munch-petersen, aust. j. exp. biol. 22:197-200, 1944) as the synergistic lysis of sheep red blood cells by staphylococcus aureus sphingomyelinase and camp factor (cohemolysin), a secreted protein from group b streptococci. we observed a camp-like reaction when bartonella henselae was grown in close proximity to s. aureus on 5% sheep blood agar. this study describes the cloning, sequencing, and characteriz ... | 2005 | 15972511 |
| new insights into metabolic properties of marine bacteria encoding proteorhodopsins. | proteorhodopsin phototrophy was recently discovered in oceanic surface waters. in an effort to characterize uncultured proteorhodopsin-exploiting bacteria, large-insert bacterial artificial chromosome (bac) libraries from the mediterranean sea and red sea were analyzed. fifty-five bacs carried diverse proteorhodopsin genes, and we confirmed the function of five. we calculate that proteorhodopsin-exploiting bacteria account for 13% of microorganisms in the photic zone. we further show that some p ... | 2005 | 16008504 |
| origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members. | we report an in-depth computational study of the protein sequences and structures of the superfamily of archaeo-eukaryotic primases (aeps). this analysis greatly expands the range of diversity of the aeps and reveals the unique active site shared by all members of this superfamily. in particular, it is shown that eukaryotic nucleo-cytoplasmic large dna viruses, including poxviruses, asfarviruses, iridoviruses, phycodnaviruses and the mimivirus, encode aeps of a distinct family, which also includ ... | 2005 | 16027112 |
| identification, characterization, and classification of genes encoding perchlorate reductase. | the reduction of perchlorate to chlorite, the first enzymatic step in the bacterial reduction of perchlorate, is catalyzed by perchlorate reductase. the genes encoding perchlorate reductase (pcrabcd) in two dechloromonas species were characterized. sequence analysis of the pcrab gene products revealed similarity to alpha- and beta-subunits of microbial nitrate reductase, selenate reductase, dimethyl sulfide dehydrogenase, ethylbenzene dehydrogenase, and chlorate reductase, all of which are type ... | 2005 | 16030201 |
| carboxyl-terminal protease regulates brucella suis morphology in culture and persistence in macrophages and mice. | the putative carboxyl-terminal processing protease (ctpa) of brucella suis 1330 is a member of a novel family of endoproteases involved in the maturation of proteins destined for the cell envelope. the b. suis ctpa protein shared up to 77% homology with ctpa proteins of other bacteria. a ctpa-deficient brucella strain (1330deltactpa), generated by allelic exchange, produced smaller colonies on enriched agar plates and exhibited a 50% decrease in growth rate in enriched liquid medium and no growt ... | 2005 | 16077124 |
| allophanate hydrolase, not urease, functions in bacterial cyanuric acid metabolism. | growth substrates containing an s-triazine ring are typically metabolized by bacteria to liberate 3 mol of ammonia via the intermediate cyanuric acid. over a 25-year period, a number of original research papers and reviews have stated that cyanuric acid is metabolized in two steps to the 2-nitrogen intermediate urea. in the present study, allophanate, not urea, was shown to be the 2-nitrogen intermediate in cyanuric acid metabolism in all the bacteria examined. six different experimental results ... | 2005 | 16085834 |
| evidence for a second class of s-adenosylmethionine riboswitches and other regulatory rna motifs in alpha-proteobacteria. | riboswitches are rna elements in the 5' untranslated leaders of bacterial mrnas that directly sense the levels of specific metabolites with a structurally conserved aptamer domain to regulate expression of downstream genes. riboswitches are most common in the genomes of low gc gram-positive bacteria (for example, bacillus subtilis contains examples of all known riboswitches), and some riboswitch classes seem to be restricted to this group. | 2005 | 16086852 |
| e1 enzyme of the pyruvate dehydrogenase complex in corynebacterium glutamicum: molecular analysis of the gene and phylogenetic aspects. | the e1p enzyme is an essential part of the pyruvate dehydrogenase complex (pdhc) and catalyzes the oxidative decarboxylation of pyruvate with concomitant acetylation of the e2p enzyme within the complex. we analyzed the corynebacterium glutamicum acee gene, encoding the e1p enzyme, and constructed and characterized an e1p-deficient mutant. sequence analysis of the c. glutamicum acee gene and adjacent regions revealed that acee is not flanked by genes encoding other enzymes of the pdhc. transcrip ... | 2005 | 16109942 |
| requirements for heterologous production of a complex metalloenzyme: the membrane-bound [nife] hydrogenase. | by taking advantage of the tightly clustered genes for the membrane-bound [nife] hydrogenase of ralstonia eutropha h16, broad-host-range recombinant plasmids were constructed carrying the entire membrane-bound hydrogenase (mbh) operon encompassing 21 genes. we demonstrate that the complex mbh biosynthetic apparatus is actively produced in hydrogenase-free hosts yielding fully assembled and functional mbh protein. | 2005 | 16159796 |
| a hypervariable 130-kilobase genomic region of magnetospirillum gryphiswaldense comprises a magnetosome island which undergoes frequent rearrangements during stationary growth. | genes involved in magnetite biomineralization are clustered in the genome of the magnetotactic bacterium magnetospirillum gryphiswaldense. we analyzed a 482-kb genomic fragment, in which we identified an approximately 130-kb region representing a putative genomic "magnetosome island" (mai). in addition to all known magnetosome genes, the mai contains genes putatively involved in magnetosome biomineralization and numerous genes with unknown functions, as well as pseudogenes, and it is particularl ... | 2005 | 16237001 |
| four-helix bundle: a ubiquitous sensory module in prokaryotic signal transduction. | motivation: transmembrane chemoreceptors in escherichia coli utilize ligand-binding domains for detecting various external signals. the structure of this domain in the e.coli aspartate receptor, tar, is known and its signal transduction mechanism is under investigation. current domain models for this important sensory module are inaccurate and, therefore, cannot reveal the distribution of this domain within the current genomic landscape. results: we carried out sensitive and exhaustive psi-blast ... | 2005 | 16306392 |
| a lithium-sensitive and sodium-tolerant 3'-phosphoadenosine-5'-phosphatase encoded by hala from the cyanobacterium arthrospira platensis is closely related to its counterparts from yeasts and plants. | 3'-phosphoadenosine-5'-phosphatase (papase) is required for the removal of toxic 3'-phosphoadenosine-5'-phosphate (pap) produced during sulfur assimilation in various eukaryotic organisms. this enzyme is a well-known target of lithium and sodium toxicity and has been used for the production of salt-resistant transgenic plants. in addition, papase has also been proposed as a target in the treatment of manic-depressive patients. one gene, hala, which could encode a protein closely related to the p ... | 2006 | 16391050 |
| expression cloning and periplasmic orientation of the francisella novicida lipid a 4'-phosphatase lpxf. | francisella tularensis and related intracellular pathogens synthesize lipid a molecules that differ from their escherichia coli counterparts. although a functional orthologue of lpxk, the gene encoding the lipid a 4'-kinase, is present in francisella, no 4'-phosphate moiety is attached to francisella lipid a. we now demonstrate that a membrane-bound phosphatase present in francisella novicida u112 selectively removes the 4'-phosphate residue from tetra- and pentaacylated lipid a molecules. a clo ... | 2006 | 16467300 |
| crystallization and preliminary x-ray crystallographic analysis of the glur0 ligand-binding core from nostoc punctiforme. | glur0 from nostoc punctiforme (npglur0) is a bacterial homologue of the ionotropic glutamate receptor. the ligand-binding core of npglur0 was crystallized at 294 k using the hanging-drop vapour-diffusion method. the l-glutamate-complexed crystal belongs to space group c222(1), with unit-cell parameters a = 78.0, b = 145.1, c = 132.1 a. the crystals contain three subunits in the asymmetric unit, with a vm value of 2.49 a3 da(-1). the diffraction limit of the l-glutamate complex data set was 2.1 a ... | 2005 | 16511224 |
| oxygen-dependent regulation of the central pathway for the anaerobic catabolism of aromatic compounds in azoarcus sp. strain cib. | the role of oxygen in the transcriptional regulation of the pn promoter that controls the bzd operon involved in the anaerobic catabolism of benzoate in the denitrifying azoarcus sp. strain cib has been investigated. in vivo experiments using pn::lacz translational fusions, in both azoarcus sp. strain cib and escherichia coli cells, have shown an oxygen-dependent repression effect on the transcription of the bzd catabolic genes. e. coli fnr was required for the anaerobic induction of the pn prom ... | 2006 | 16547020 |
| aerobic benzoyl-coenzyme a (coa) catabolic pathway in azoarcus evansii: conversion of ring cleavage product by 3,4-dehydroadipyl-coa semialdehyde dehydrogenase. | benzoate, a strategic intermediate in aerobic aromatic metabolism, is metabolized in various bacteria via an unorthodox pathway. the intermediates of this pathway are coenzyme a (coa) thioesters throughout, and ring cleavage is nonoxygenolytic. the fate of the ring cleavage product 3,4-dehydroadipyl-coa semialdehyde was studied in the beta-proteobacterium azoarcus evansii. cell extracts contained a benzoate-induced, nadp(+)-specific aldehyde dehydrogenase, which oxidized this intermediate. a pos ... | 2006 | 16585753 |
| the genome of rhizobium leguminosarum has recognizable core and accessory components. | rhizobium leguminosarum is an alpha-proteobacterial n2-fixing symbiont of legumes that has been the subject of more than a thousand publications. genes for the symbiotic interaction with plants are well studied, but the adaptations that allow survival and growth in the soil environment are poorly understood. we have sequenced the genome of r. leguminosarum biovar viciae strain 3841. | 2006 | 16640791 |
| spatial localizations of mam22 and mam12 in the magnetosomes of magnetospirillum magnetotacticum. | magnetospirillum magnetotacticum possesses intracellular magnetite particles with a chain-like structure, termed magnetosomes. the bacterium expresses 22-kda and 12-kda magnetosome-associated proteins, termed mam22 (mama) and mam12 (mamc), respectively. in this study, we investigated the structure of the purified magnetosomes with transmission electron microscopic techniques and found that the magnetosomes consisted of four compartments, i.e., magnetite crystal, magnetosomal membrane, interparti ... | 2006 | 16707673 |
| quantifying the magnetic advantage in magnetotaxis. | magnetotactic bacteria are characterized by the production of magnetosomes, nanoscale particles of lipid bilayer encapsulated magnetite, that act to orient the bacteria in magnetic fields. these magnetosomes allow magneto-aerotaxis, which is the motion of the bacteria along a magnetic field and toward preferred concentrations of oxygen. magneto-aerotaxis has been shown to direct the motion of these bacteria downward toward sediments and microaerobic environments favorable for growth. herein, we ... | 2006 | 16714352 |
| glycosylation of b-type flagellin of pseudomonas aeruginosa: structural and genetic basis. | the flagellin of pseudomonas aeruginosa can be classified into two major types-a-type or b-type-which can be distinguished on the basis of molecular weight and reactivity with type-specific antisera. flagellin from the a-type strain pak was shown to be glycosylated with a heterogeneous o-linked glycan attached to thr189 and ser260. here we show that b-type flagellin from strain pao1 is also posttranslationally modified with an excess mass of up to 700 da, which cannot be explained through phosph ... | 2006 | 16740946 |
| genetic analysis of the requirement for flp-2, tadv, and rcpb in actinobacillus actinomycetemcomitans biofilm formation. | the tad locus of actinobacillus actinomycetemcomitans encodes a molecular transport system required for tenacious, nonspecific adherence to surfaces and formation of extremely strong biofilms. this locus is dedicated to the biogenesis of flp pili, which are required for colonization and virulence. we have previously shown that 11 of the 14 tad locus genes are required for adherence and flp pilus production. here, we present genetic and phylogenetic analyses of flp-2, tadv, and rcpb genes in biof ... | 2006 | 16923904 |
| tungsten transport protein a (wtpa) in pyrococcus furiosus: the first member of a new class of tungstate and molybdate transporters. | a novel tungstate and molybdate binding protein has been discovered from the hyperthermophilic archaeon pyrococcus furiosus. this tungstate transport protein a (wtpa) is part of a new abc transporter system selective for tungstate and molybdate. wtpa has very low sequence similarity with the earlier-characterized transport proteins moda for molybdate and tupa for tungstate. its structural gene is present in the genome of numerous archaea and some bacteria. the identification of this new tungstat ... | 2006 | 16952940 |
| transcriptional organization and regulation of magnetosome operons in magnetospirillum gryphiswaldense. | genes involved in magnetite biomineralization are clustered within the genomic magnetosome island of magnetospirillum gryphiswaldense. their transcriptional organization and regulation were studied by several approaches. cotranscription of genes within the mamab, mamdc, and mms clusters was demonstrated by reverse transcription-pcr (rt-pcr) of intergenic regions, indicating the presence of long polycistronic transcripts extending over more than 16 kb. the transcription start points of the mamab, ... | 2006 | 16957191 |
| the crystal structure of the e. coli stress protein ycif. | ycif is a protein that is up-regulated when bacteria experience stress conditions, and is highly conserved in a range of bacterial species. ycif has no known structure or biochemical function. to learn more about its potential molecular function and its role in the bacterial stress response, we solved the crystal structure of ycif at 2.0 angstrom resolution by the multiple wavelength anomalous diffraction (mad) technique. ycif is a dimer in solution, and forms a homodimer in the crystal asymmetr ... | 2006 | 17001035 |
| hemoglobin degradation in malaria-infected erythrocytes determined from live cell magnetophoresis. | during intra-erythrocytic development, malaria trophozoites digest hemoglobin, which leads to parasite growth and asexual replication while accumulating toxic heme. to avoid death, the parasite synthesizes insoluble hemozoin crystals in the digestive vacuole through polymerization of beta-hematin dimers. in the process, the heme is converted to a high-spin ferriheme whose magnetic properties were studied as early as 1936 by pauling et al. here, by magnetophoretic cell motion analysis, we provide ... | 2006 | 16461330 |
| biogenesis of actin-like bacterial cytoskeletal filaments destined for positioning prokaryotic magnetic organelles. | magnetosomes comprise a magnetic nanocrystal surrounded by a lipid bilayer membrane. these unique prokaryotic organelles align inside magnetotactic bacterial cells and serve as an intracellular compass allowing the bacteria to navigate along the geomagnetic field in aquatic environments. cryoelectron tomography of magnetospirillum strains has revealed that the magnetosome chain is surrounded by a network of filaments that may be composed of mamk given that the filaments are absent in the mamk mu ... | 2006 | 17085581 |
| cyclohexa-1,5-diene-1-carbonyl-coenzyme a (coa) hydratases of geobacter metallireducens and syntrophus aciditrophicus: evidence for a common benzoyl-coa degradation pathway in facultative and strict anaerobes. | in the denitrifying bacterium thauera aromatica, the central intermediate of anaerobic aromatic metabolism, benzoyl-coenzyme a (coa), is dearomatized by the atp-dependent benzoyl-coa reductase to cyclohexa-1,5-diene-1-carbonyl-coa (dienoyl-coa). the dienoyl-coa is further metabolized by a series of beta-oxidation-like reactions of the so-called benzoyl-coa degradation pathway resulting in ring cleavage. recently, evidence was obtained that obligately anaerobic bacteria that use aromatic growth s ... | 2007 | 17122342 |
| cyclohexa-1,5-diene-1-carbonyl-coenzyme a (coa) hydratases of geobacter metallireducens and syntrophus aciditrophicus: evidence for a common benzoyl-coa degradation pathway in facultative and strict anaerobes. | in the denitrifying bacterium thauera aromatica, the central intermediate of anaerobic aromatic metabolism, benzoyl-coenzyme a (coa), is dearomatized by the atp-dependent benzoyl-coa reductase to cyclohexa-1,5-diene-1-carbonyl-coa (dienoyl-coa). the dienoyl-coa is further metabolized by a series of beta-oxidation-like reactions of the so-called benzoyl-coa degradation pathway resulting in ring cleavage. recently, evidence was obtained that obligately anaerobic bacteria that use aromatic growth s ... | 2007 | 17122342 |
| the bacterial actin-like cytoskeleton. | recent advances have shown conclusively that bacterial cells possess distant but true homologues of actin (mreb, parm, and the recently uncovered mamk protein). despite weak amino acid sequence similarity, mreb and parm exhibit high structural homology to actin. just like f-actin in eukaryotes, mreb and parm assemble into highly dynamic filamentous structures in vivo and in vitro. mreb-like proteins are essential for cell viability and have been implicated in major cellular processes, including ... | 2006 | 17158703 |
| loss of a universal trna feature. | trna(his) has thus far always been found with one of the most distinctive of trna features, an extra 5' nucleotide that is usually a guanylate. trna(his) genes in a disjoint alphaproteobacterial group comprising the rhizobiales, rhodobacterales, caulobacterales, parvularculales, and pelagibacter generally fail to encode this extra guanylate, unlike those of other alphaproteobacteria and bacteria in general. rather than adding an extra 5' guanylate posttranscriptionally as eukaryotes do, evidence ... | 2007 | 17172343 |
| loss of a universal trna feature. | trna(his) has thus far always been found with one of the most distinctive of trna features, an extra 5' nucleotide that is usually a guanylate. trna(his) genes in a disjoint alphaproteobacterial group comprising the rhizobiales, rhodobacterales, caulobacterales, parvularculales, and pelagibacter generally fail to encode this extra guanylate, unlike those of other alphaproteobacteria and bacteria in general. rather than adding an extra 5' guanylate posttranscriptionally as eukaryotes do, evidence ... | 2007 | 17172343 |
| identification of important regions for ethylene binding and signaling in the transmembrane domain of the etr1 ethylene receptor of arabidopsis. | the ethylene binding domain (ebd) of the arabidopsis thaliana etr1 receptor is modeled as three membrane-spanning helices. we surveyed ethylene binding activity in different kingdoms and performed a bioinformatic analysis of the ebd. ethylene binding is confined to land plants, chara, and a group of cyanobacteria but is largely absent in other organisms, consistent with our finding that ebd-like sequences are overrepresented among plant and cyanobacterial species. we made amino acid substitution ... | 2006 | 17189345 |
| characterization of the variants, flanking genes, and promoter activity of the leifsonia xyli subsp. cynodontis insertion sequence is1237. | we performed a comprehensive study of the distribution and function of an insertion sequence (is) element, is1237, in the genome of leifsonia xyli subsp. cynodontis, a useful genetic carrier for expressing beneficial foreign genes in plants. two shorter is1237 isoforms, is1237d1 and is1237d2 resulting from precise deletion between two nonperfect repeats, were found in the bacterial genome at a level that was one-fifth the level of wild-type is1237. both the genome and native plasmid pcxc100 harb ... | 2007 | 17293427 |